David Humphreys

Hi Mathavanpu, If am not sure where you identify a file called "hg19_ref_all.txt", can you let me know? The annotation steps are documented in vignette (or via https://github.com/VCCRI/Sierra/wiki/Sierra-Vignette) and do...

Hi Dario, Can you confirm this is the case for the TwoSzabo data set? If TwoSzabo data sets works can you let me know if you analysing STAR/CIRI/CircExplorer output? If...

Good suggestions. I have started to look at test data set. The MUC7 example doesn't look like a BSJ, but rather a forward splice junction. I need to work out...

Any chance you could attach a couple of sequences from fastq file. This will be useful sanity check. For example the following read IDs would be useful: A00121:71:HFFY2DSXX:2:1106:11776:28745 A00121:71:HFFY2DSXX:2:1124:22236:36495 A00121:71:HFFY2DSXX:2:1146:19090:8844

When I blat each of those reads it shows that they are indeed canonical junctions (see image below). Given that the CIGAR strings in chimeric junction output also suggested that...

[Submitted issue](https://github.com/alexdobin/STAR/issues/852) to STAR.

Hi Yuna, Thanks for identifying this issue. I have amended this so that the correct output is generated for CIRI data. This issue has reminded me that the BSJ sequence...

Hi Dario, There are a number of tables that can be built through Gene View tab. I am assuming you are refering to the "Grouped" table output using STAR chimeric...

Hi Shan, It appears as if the yaml library may not have updated as message says cannot remove prior installation. Can you cehck what version of yaml is installed, this...

Run just the following command BiocManager::install(c("BSgenome.Hsapiens.UCSC.hg19", # Genome; enables sequence analysis "TxDb.Hsapiens.UCSC.hg19.knownGene", # Transcript database "org.Hs.eg.db"))